Abstract: Factors affecting ISSR-PCR amplification of longan(Dimocarpus Longan Lour.) were optimized in this study and ISSR system for longan was established. Each 20uL amplification reaction consisted of 25ng DNA, 0.2 μ mol/L primer, 100 μmol/L each of dNTP, 0.5U Taq DNA polymerase, 2.5 mmol/L MgCl2 and 2.0 μl 10×PCR buffer; Amplification was under the following conditions: 5 min at 94℃ for 1 cycle, followed by 1 min at 94℃, 1 min at annealing temperature, and 90s at 72℃ for 40 cycles, and 7 min at 72℃ for a final extension.